double precision function rmsnat(ib,jcon,iref,iprot)
      implicit none
      include 'DIMENSIONS'
      include 'DIMENSIONS.ZSCOPT'
      include 'COMMON.IOUNITS'
      include 'COMMON.COMPAR'
      include 'COMMON.CHAIN' 
      include 'COMMON.INTERACT'
      include 'COMMON.VAR'
      double precision creff(3,maxres2),cc(3,maxres2)
      double precision przes(3),obrot(3,3)
      logical non_conv
      integer ishif,i,ii,j,jcon,ib,iref,iprot
      double precision rms
      if (caonly(iprot)) then
        call fitsq(rms,c(1,nstart_sup(iprot)),cref(1,nstart_sup(iprot),
     &  iref,ib,iprot),nsup(iprot),przes,obrot,non_conv)
      else if (sconly(iprot)) then
        call fitsq(rms,c(1,nstart_sup(iprot)+nres),
     &    cref(1,nstart_sup(iprot)+nres,iref,ib,
     &    iprot),nsup(iprot),przes,obrot,non_conv)
      else
        ii=0
        do i=nstart_sup(iprot),nend_sup(iprot)
          ii=ii+1
          do j=1,3
            cc(j,ii)=c(j,i)
            creff(j,ii)=cref(j,i,iref,ib,iprot)
          enddo
        enddo
        do i=nstart_sup(iprot),nend_sup(iprot)
          if (itype(i).ne.10 .and. itype(i).ne.21) then
            ii=ii+1
            do j=1,3
              cc(j,ii)=c(j,i+nres)
              creff(j,ii)=cref(j,i+nres,iref,ib,iprot)
            enddo
          endif
        enddo
        call fitsq(rms,cc(1,1),creff(1,1),ii,przes,obrot,non_conv)
      endif
      if (non_conv) then
        print *,'Error: FITSQ non-convergent, jcon',jcon
        rmsnat=1.0d2
      else if (rms.lt.-1.0d-6) then 
        print *,'Error: rms^2 = ',rms,jcon
        rmsnat = 1.0d2
      else if (rms.ge.1.0d-6 .and. rms.lt.0) then
        rmsnat=0.0d0
      else 
        rmsnat = dsqrt(rms)
      endif
      return
      end